First of all, I would like to thank Pete @petebankhead very much for creating QuPath, it is amazing!
I am trying to quantify IHC staining + intensity for proteins located in the extracellular compartment in whole scanned sections.
Tumour positive staining percentage, stroma positive staining percentage, tumour+stroma positive staining percentage plus stain intensity, and H-score >>> similar to to the data produced by the cell classifier, but extracellularly.
I have tried positive cell detections + cell classifier. I think, QuPath is counting positive cells in the regions of interest (whole section), not measuring the whole area where any signal is observed. This was apparent from the data generated. I have performed some checks by eye on a few random slides, I found that, by focusing on counting positive cells only, most of the staining observed in the stroma architecture, which is extracellular, was missed.
I have also tried: positive cell detections + pixel classifier, however, the results table showed: % of tumour and % of stroma within the section separately from positive %, and negative % , and did not take into account all measurement to produce the tumour positive % and stroma positive % like the data generated using the cell classifier.
I would very much appreciate ideas to achieve my analysis goal please.